How can I make multiple meshes into a single hollow mesh?
For separate meshes, you should first of all join them in a single object (ctrlJ)

Then, if in that object you have separate "islands" of faces (like eyeballs and body) you can either:


join them manually, adding new geometry, or joining existing 
make (eg) eyeballs intersect body by enlarging or reducing any of them, and then use a boolean modifier with "union" to get a single, "manifold" mesh (check very well normals before using booleans, and to not have negative scale, since that would invert normals effect in the boolean). Needs some practice with simpler object.
to remove "interior geometry" I have no other solution then removing it manually, eventually closing open surfaces left inside (there could be some, since the model was thought for a usage (render, animation) for which this was not a problem). 
anyway, since you're creating stl, I guess you are going to print the object, so, you can surely have some help before exporting by using the "3d print toolbox" addon (included, but not enabled by default) to find and correct problematic shapes. And after export, the print program tipically have some "correction" tool to fix minor problems.